Abstarct: Every organization needs changes to improve efficiency and stay in the competitive. Organizations often need to implement changes in management, design and delivery of services. Persistent changes in educational environments is considered as an important challenge for managers and change management is one of the main topics of management science nowadays. Change management as a deliberate set of activities that facilitate and support the success of individual and organizational change and the realization of its intended business results. Applying change is necessary for organizational improvement. The purpose of present research was to investigate the challenges of change in physical education faculties in Iran that was done with qualitative method (Grounded Theory and interview). The participants were 13 managers and faculty members of physical education faculties who were selected via snow ball method. Data collection was done by using semi-structured interviews and they were analyzed using conventional content analysis method. After each interview, conceptual codes were extracted and put in several main themes therefore 21 concept codes were lodged in 3 main themes: external environment, internal environment and changed process. The validity and reliability of the study were baxsed on the four dimensions of Credibility, Transferability, Dependability and conformability. The results showed that the challenges of managing change in physical education faculties was the most important code which reasons could be lack of proper education of change management, the policy and government-affiliated universities, resistance to change and main focuses of management and executive management. According to the research results, managers should consider proper programs in order to make changes also getting well designed responses to challenges of change.